miEAA: microRNA enrichment analysis and annotation

Abstract

Similar to the development of gene set enrichment and gene regulatory network analysis tools over a decade ago, microRNA enrichment tools are currently gaining importance. Building on our experience with the gene set analysis toolkit GeneTrail, we implemented the miRNA Enrichment Analysis and Annotation tool (miEAA). MiEAA is a web-based application that offers a variety of commonly applied statistical tests such as over-representation analysis and miRNA set enrichment analysis, which is similar to Gene Set Enrichment Analysis. Besides the different statistical tests, miEAA also provides rich functionality in terms of miRNA categories. Altogether, over 14 000 miRNA sets have been added, including pathways, diseases, organs and target genes. Importantly, our tool can be applied for miRNA precursors as well as mature miRNAs. To make the tool as useful as possible we additionally implemented supporting tools such as converters between different miRBase versions and converters from miRNA names to precursor names. We evaluated the performance of miEAA on two sets of miRNAs that are affected in lung adenocarcinomas and have been detected by array analysis. The web-based application is freely accessible at: http://www.ccb.uni-saarland.de/mieaa_tool/.

Figure 1.

Workflow of miEAA. Input for miEAA are either miRNA or precursor names from miRBase version 21. After uploading a plain text file containing these names, the user can chose the enrichment method: ORA or GSEA. Depending on this choice, the user can provide an own reference set for ORA. For GSEA, the input list must be sorted by a meaningful criterion. In a last step, the user can choose the categories that should be analyzed, as well as the P-value significance threshold and adjustment method. After computation, the results are presented in a tabular format on an HTML web site and can also be downloaded as Excel sheet or tab-separated text file.

Figure 2.

Example of an ORA for miRNA input. This screenshot visualizes an example, where we analyzed a set of miRNAs with ORA as enrichment method. The output has a tabular format containing the category (e.g. target genes from miRTarbase), subcategories (e.g. a certain target gene), the P-value, the miRNAs from the test set that are contained in the subcategory, the type of enrichment, the number of miRNAs that we would expect to find and the number of miRNAs that we actually observed.